Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby Joe Breitkreutz, Gary C. Hon, Chad L. Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G. Troyanskya, Trey Ideker, Kara Dolinski, Nizar N. Batada, Mike Tyers

Research output: Contribution to journalArticle

258 Scopus citations

Abstract

Background. The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results. We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases. Conclusion. Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks.

Original languageEnglish (US)
Article number11
JournalJournal of Biology
Volume5
DOIs
StatePublished - Dec 1 2006

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Fingerprint Dive into the research topics of 'Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae'. Together they form a unique fingerprint.

  • Cite this

    Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., & Tyers, M. (2006). Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of Biology, 5, [11]. https://doi.org/10.1186/jbiol36